diff --git a/libcodonusage/libcodonusage.py b/libcodonusage/libcodonusage.py index 8b136fc0d3586466c7954634030c20da221b0af2..d839d896102ec157857575c0095afcd0e95ff9a6 100644 --- a/libcodonusage/libcodonusage.py +++ b/libcodonusage/libcodonusage.py @@ -352,7 +352,7 @@ SUZUKI_DOI = "10.1016/j.febslet.2005.10.032" SUZUKI_LINK = f"[Suzuki et al (2005)](https://doi.org/{SUZUKI_DOI})" -def gene_wide_codon_usage(codon_counts, verbose=False, return_props=False): +def gene_wide_codon_usage(codon_counts, verbose=False, return_more=False): """ Compute codon usage biases "gene-wide" as the standardized difference between a gene's codon proportions and global @@ -414,12 +414,16 @@ across genes) so that they are more comparable between codons. # standardized_codon_usage_biases.style.hide(axis="index") if verbose: display(standardized_codon_usage_biases.head(3)) - if return_props: - return (standardized_codon_usage_biases, codon_proportions) + if return_more: + return { + "biases": standardized_codon_usage_biases, + "proportions": codon_proportions, + "global_proportions": global_proportions} return standardized_codon_usage_biases -def by_aa_codon_usage(codon_counts, verbose=False, return_props=False): +# TODO: add option to output RSCU instead of / besides proportions +def by_aa_codon_usage(codon_counts, verbose=False, return_more=False): """ Compute codon usage biases "by amino-acid" as the standardized difference between a gene's codon proportions and global @@ -497,12 +501,15 @@ across genes) so that they are more comparable between codons. # standardized_codon_usage_biases.style.hide(axis="index") if verbose: display(standardized_codon_usage_biases.head(3)) - if return_props: - return (standardized_codon_usage_biases, codon_proportions) + if return_more: + return { + "biases": standardized_codon_usage_biases, + "proportions": codon_proportions, + "global_proportions": global_proportions} return standardized_codon_usage_biases -def aa_usage(codon_counts, verbose=False, return_props=False): +def aa_usage(codon_counts, verbose=False, return_more=False): """ Compute amino-acid usage biases as the standardized difference between a gene's amino-acid proportions @@ -567,8 +574,11 @@ across genes) so that they are more comparable between amino-acids. # standardized_aa_usage_biases.style.hide(axis="index") if verbose: display(standardized_aa_usage_biases.head(3)) - if return_props: - return (standardized_aa_usage_biases, aa_proportions) + if return_more: + return { + "biases": standardized_aa_usage_biases, + "proportions": aa_proportions, + "global_proportions": global_aa_proportions} return standardized_aa_usage_biases